Rigify is using all Layers
Bone layers  are different from object layers.
As i can see from your screenshot, Rigfy has correctly put the bones in different bone layers, to help selection groups when animating, but the "problem" you point at is the fact that all object layers appear "occupied".
You can go to the outliner window (or create one), change the pop-up menu from "All scenes" to "visible layers", select one object layer at time and read in the outliner what's inside, to understand the thing, that - I don't think - is produced by Rigify.

Also, before pushing the "generate" button, apply the scale (Ctrl A) to both your model and the meta-rig.